R/stanmodels.R

In mlm4omics: Multilevel Model for Multivariate Responses with Missing Values

# Part of the mlm4omics package for estimating model parameters
# Copyright (C) 2015, 2016, 2017 Trustees of Columbia University
# 
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 3
# of the License, or (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public
# License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
# MA  02110-1301, USA.
# This file is only intended to be used during the installation
#process
# nocov start
MODELS_HOME  <-  "src"
if (!file.exists(MODELS_HOME)) MODELS_HOME  <-  sub("R$", "src",
getwd())

stan_files  <-  dir(file.path(MODELS_HOME, "stan_files"),
                pattern = "stan$", full.names = TRUE)
stanmodels  <-  lapply(stan_files, function(f) {
    model_cppname  <-  sub("\\.stan$", "", basename(f))
    stanfit  <-  rstan::stanc(f, allow_undefined = TRUE, 
                        obfuscate_model_name = FALSE)
    stanfit$model_cpp  <-  list(model_cppname = stanfit$model_name, 
                        model_cppcode = stanfit$cppcode)
    return(do.call(methods::new, args = c(stanfit[-seq_len(3)],
        Class  =  "stanmodel", 
        mk_cppmodule  =  function(x)
        get(paste0("model_", model_cppname)))))
    }
)
names(stanmodels)  <-  sub("\\.stan$", "", basename(stan_files))
rm(MODELS_HOME)
# nocov end